Hi everyone. I want to use hbonanza to analyses hydrogen bonds formation during MD simulation time for my protein-ligand complex system. Previously, I run md using GROMACS 4.6.5, further, I try to run hbonanza to analyses the hydrogen bonds pattern:
Below are the steps :
1) I try to get the multiple pdbs in a single file by using:
g_trjconv -f .xtc -o .pdb -b 60000 -e 100000 -dt 1000 -s em.tpr (so I got 40 frames in 40 ns), then,
2) I follow the hbonanza command:
python HBonanza.py -trajectory_filename .pdb -hydrogen_bond_distance_cutoff 3.0 -hydrogen_bond_angle_cutoff 30 -hydrogen_bond_frequency_cutoff 0.5 -single_frame_filename first_frame.pdb -output_basename output. -write_column O -low_frequency_color_r 255 -low_frequency_color_g 255 -low_frequency_color_b 255 -high_frequency_color_r 0 -high_frequency_color_g 255 -high_frequency_color_b 0 > visualize.tcl
I got Error :
ValueError: Invalid literal for float(): (as per attached)
Can anyone give any suggestions? Thanks :)
Hi Ermafatiha,
have you considered giving GROMACS' own tool g_hbond a try?
One of its options is the computation of hydrogen bond existence maps, giving you all the information you need to monitor H-bond formation, frequency and life time over time.
Cheerz & good luck,
Christian
Hi Ermafatiha,
Sorry, I have no experience with hbonanza. What I can suggest you is to use VMD. You can easily load the GROMACS trajectory in to it and can analyse the hbond easily. The difference between g_hbond, which is suggested by Christian, and VMD hbond calculation is that, VMD can provide you %occurrence of each calculated h-bond which you might not get from g_hbond command easily.
*caution: The geometric criteria used by VMD and GROMACS for h bond calculation is different, you can change this in both the cases but it will be good if you read the manuals of these tools.
Hope this help
Aditya
Thank you Christian and Aditya for the nice suggestion.
Recently, I have been using g_hbond command in GROMACS, but then I think it wasn't enough information that I need.
I never use VMD hbond calculation, will give a try for % of hbond occurence. Thanks again.
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